Streaming data may consist of multiple drifting concepts each having its own underlying data distribution. We present an ensemble learning based approach to handle the data streams having multiple underlying modes. We build a global set of classifiers from sequential data chunks; ensembles are then selected from this global set of classifiers, and new classifiers created if needed, to represent the current concept in the stream. The system is capable of performing any-time classification and to detect concept drift in the stream. In streaming data historic concepts are likely to reappear so we dont delete any of the historic classifiers. Instead, we judiciously select only pertinent classifiers from the global set while forming the ensemble set for a classification task.
Pseudomonas aeruginosa (PA) is a ubiquitous opportunistic pathogen that is capable of causing highly problematic, chronic infections in cystic fibrosis and chronic obstructive pulmonary disease patients. With the increased prevalence of multi-drug resistant PA, the conventional “one gene, one drug, one disease” paradigm is losing effectiveness. Network pharmacology, on the other hand, may hold the promise of discovering new drug targets to treat a variety of PA infections. However, given the urgent need for novel drug target discovery, a PA protein-protein interaction (PPI) network of high accuracy and coverage, has not yet been constructed. In this study, we predicted a genome-scale PPI network of PA by integrating various genomic features of PA proteins/genes by a machine learning-based approach. A total of 54,107 interactions covering 4,181 proteins in PA were predicted. A high-confidence network combining predicted high-confidence interactions, a reference set and verified interactions that consist of 3,343 proteins and 19,416 potential interactions was further assembled and analyzed. The predicted interactome network from this study is the first large-scale PPI network in PA with significant coverage and high accuracy. Subsequent analysis, including validations based on existing small-scale PPI data and the network structure comparison with other model organisms, shows the validity of the predicted PPI network. Potential drug targets were identified and prioritized based on their essentiality and topological importance in the high-confidence network. Host-pathogen protein interactions between human and PA were further extracted and analyzed. In addition, case studies were performed on protein interactions regarding anti-sigma factor MucA, negative periplasmic alginate regulator MucB, and the transcriptional regulator RhlR. A web server to access the predicted PPI dataset is available at http://research.cchmc.org/PPIdatabase/.
Formal concept analysis (FCA) has been applied successively in diverse fields such as data mining, conceptual modeling, social networks, software engineering, and the semantic web. One shortcoming of FCA, however, is the large number of concepts that typically arise in dense datasets hindering typical tasks such as rule generation and visualization. To overcome this shortcoming, it is important to develop formalisms and methods to segment, categorize and cluster formal concepts. The first step in achieving these aims is to define suitable similarity and dissimilarity measures of formal concepts. In this paper we propose three similarity measures based on existent set-based measures in addition to developing the completely novel zeros-induced measure. Moreover, we formally prove that all the measures proposed are indeed similarity measures and investigate the computational complexity of computing them. Finally, an extensive empirical evaluation on real-world data is presented in which the utility and character of each similarity measure is tested and evaluated.
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